chmiel_human_rnaseq

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2022-03-08, 18:04 based on data in:

/share/biocore/projects/Zeki_A_UCD/2022_Zeki_Chmiel_Human_RNAseq/00-RawData
/share/biocore/projects/Zeki_A_UCD/2022_Zeki_Chmiel_Human_RNAseq/01-HTS_Prepro
/share/biocore/projects/Zeki_A_UCD/2022_Zeki_Chmiel_Human_RNAseq/02-STAR_alignment
/share/biocore/projects/Zeki_A_UCD/2022_Zeki_Chmiel_Human_RNAseq/03-MultiQC

General Statistics

Showing ¹²/₁₂ rows and ²/₂ columns.

Sample Name	% Aligned	M Aligned
ZEKI0001	91.5%	15.6
ZEKI0002	91.7%	12.2
ZEKI0003	91.2%	17.1
ZEKI0004	91.0%	17.3
ZEKI0005	90.8%	19.4
ZEKI0006	91.2%	16.5
ZEKI0007	91.5%	17.4
ZEKI0008	91.1%	17.3
ZEKI0009	91.0%	14.4
ZEKI0010	92.7%	19.9
ZEKI0011	90.7%	14.2
ZEKI0012	90.3%	13.3

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|		STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count

STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

Gene Counts

Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

HTStream

HTStream quality control and processing pipeline for High Throughput Sequencing data.

Processing Overview

General statistics from the HTStream pipeline.

Preprocessing Statistics

Fragment Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

Basepair Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

hts_Stats

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ¹²/₁₂ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
ZEKI0001	100.00%	92.82%	93.58%	45.84%	0.0020%	initial stats
ZEKI0002	100.00%	93.19%	93.68%	46.83%	0.0020%	initial stats
ZEKI0003	100.00%	92.54%	93.28%	46.42%	0.0020%	initial stats
ZEKI0004	100.00%	93.09%	93.23%	46.78%	0.0020%	initial stats
ZEKI0005	100.00%	93.07%	92.98%	46.30%	0.0021%	initial stats
ZEKI0006	100.00%	93.19%	93.27%	46.33%	0.0021%	initial stats
ZEKI0007	100.00%	93.01%	93.39%	46.86%	0.0021%	initial stats
ZEKI0008	100.00%	93.19%	93.15%	46.69%	0.0021%	initial stats
ZEKI0009	100.00%	92.71%	93.21%	47.51%	0.0018%	initial stats
ZEKI0010	100.00%	93.83%	93.93%	46.14%	0.0021%	initial stats
ZEKI0011	100.00%	92.88%	93.18%	46.47%	0.0020%	initial stats
ZEKI0012	100.00%	92.28%	92.28%	46.91%	0.0020%	initial stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction1`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q301`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q301`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content1`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content1`	None
\|\|	Notes	Notes	Notes	`St_Notes1`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Notice: Each sample has a uniform read length distribution.

Showing ¹²/₁₂ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
ZEKI0001	151	151
ZEKI0002	151	151
ZEKI0003	151	151
ZEKI0004	151	151
ZEKI0005	151	151
ZEKI0006	151	151
ZEKI0007	151	151
ZEKI0008	151	151
ZEKI0009	151	151
ZEKI0010	151	151
ZEKI0011	151	151
ZEKI0012	151	151

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		R1 Read Lengths	R1 Read Lengths	Length of R1 reads (uniform for each sample).	`St_Read_Lengths_R1_24994158790936`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_24994158790936`	None

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

hts_SeqScreener

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Notice: No hits in any sample.

hts_SeqScreener 2

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Showing ¹²/₁₂ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits	Notes
ZEKI0001	461718	2.0041%	count the number of rRNA reads
ZEKI0002	513050	2.8639%	count the number of rRNA reads
ZEKI0003	684027	2.6317%	count the number of rRNA reads
ZEKI0004	735292	2.7065%	count the number of rRNA reads
ZEKI0005	851865	2.8336%	count the number of rRNA reads
ZEKI0006	768117	3.0535%	count the number of rRNA reads
ZEKI0007	734308	2.8445%	count the number of rRNA reads
ZEKI0008	770198	2.8899%	count the number of rRNA reads
ZEKI0009	727821	3.2198%	count the number of rRNA reads
ZEKI0010	659214	2.3050%	count the number of rRNA reads
ZEKI0011	507109	2.4175%	count the number of rRNA reads
ZEKI0012	555590	2.8266%	count the number of rRNA reads

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Sort	Group	Column	Description	ID	Scale
\|\|	PE hits	PE hits	Number of Paired End Reads with Sequence	`Ss_PE_hits2`	None
\|\|	% PE Lost	% PE Hits	Percentage of Paired End Reads Lost	`Ss_PE_%_hits2`	None
\|\|	Notes	Notes	Notes	`Ss_Notes2`	None

hts_SuperDeduper

A reference free duplicate read removal tool.

Showing ¹²/₁₂ rows and ³/₃ columns.

Sample Name	% Duplicates	% Ignored	Notes
ZEKI0001	25.67%	0.01%	remove dups
ZEKI0002	25.46%	0.01%	remove dups
ZEKI0003	27.33%	0.01%	remove dups
ZEKI0004	29.57%	0.01%	remove dups
ZEKI0005	28.56%	0.01%	remove dups
ZEKI0006	27.46%	0.01%	remove dups
ZEKI0007	25.98%	0.01%	remove dups
ZEKI0008	28.42%	0.01%	remove dups
ZEKI0009	29.36%	0.01%	remove dups
ZEKI0010	24.57%	0.01%	remove dups
ZEKI0011	25.23%	0.01%	remove dups
ZEKI0012	24.66%	0.01%	remove dups

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Sort	Group	Column	Description	ID	Scale
\|\|	% Duplicates	% Duplicates	Percentage of Duplicate Reads (SE and PE)	`Sd_%_Duplicates1`	None
\|\|	% Ignored	% Ignored	Percentage of Ignored Reads (SE and PE)	`Sd_%_Ignored1`	None
\|\|	Notes	Notes	Notes	`Sd_Notes1`	None

SuperDeduper: Duplicate Saturation

Plots the number of duplicates against the number of unique reads per sample.

hts_AdapterTrimmer

Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

Showing ¹²/₁₂ rows and ⁴/₄ columns.

Sample Name	% Bp Lost	% Adapters	Avg. Bps Trimmed	Notes
ZEKI0001	8.08%	73.95%	33.02	trim adapters
ZEKI0002	9.66%	82.02%	35.58	trim adapters
ZEKI0003	9.62%	81.00%	35.87	trim adapters
ZEKI0004	10.25%	84.49%	36.65	trim adapters
ZEKI0005	10.70%	85.56%	37.78	trim adapters
ZEKI0006	11.14%	87.67%	38.37	trim adapters
ZEKI0007	10.01%	82.80%	36.53	trim adapters
ZEKI0008	10.23%	84.23%	36.69	trim adapters
ZEKI0009	10.53%	85.42%	37.23	trim adapters
ZEKI0010	8.50%	76.91%	33.36	trim adapters
ZEKI0011	9.16%	79.16%	34.96	trim adapters
ZEKI0012	10.34%	84.21%	37.08	trim adapters

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`At_%_BP_Lost1`	None
\|\|	% Adapters	% Adapters	Percentage of Reads (SE and PE) with an Adapter	`At_%_Adapters1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of basepairs trimmed from reads	`At_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`At_Notes1`	None

AdapterTrimmer: Trimmed Basepairs Composition

Composition of basepairs trimmed from the ends of paired end and single end reads.

hts_QWindowTrim

Uses a sliding window approach to remove the low quality ends of reads.

Showing ¹²/₁₂ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
ZEKI0001	0.22%	47.21%	52.79%	0.61	quality trim the ends of reads
ZEKI0002	0.21%	48.74%	51.26%	0.58	quality trim the ends of reads
ZEKI0003	0.27%	41.46%	58.54%	0.74	quality trim the ends of reads
ZEKI0004	0.26%	39.90%	60.10%	0.71	quality trim the ends of reads
ZEKI0005	0.26%	40.47%	59.53%	0.71	quality trim the ends of reads
ZEKI0006	0.24%	42.57%	57.43%	0.65	quality trim the ends of reads
ZEKI0007	0.25%	35.87%	64.13%	0.68	quality trim the ends of reads
ZEKI0008	0.24%	41.27%	58.73%	0.65	quality trim the ends of reads
ZEKI0009	0.28%	38.13%	61.87%	0.75	quality trim the ends of reads
ZEKI0010	0.18%	41.20%	58.80%	0.51	quality trim the ends of reads
ZEKI0011	0.28%	39.14%	60.86%	0.78	quality trim the ends of reads
ZEKI0012	0.30%	38.16%	61.84%	0.81	quality trim the ends of reads

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Qt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R2_BP_Lost1`	None
\|\|	Avg. Bpss Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Qt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Qt_Notes1`	None

QWindowTrim: Trimmed Basepairs Composition

Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

hts_PolyATTrim

Attempts to trim poly-A and poly-T sequences from the end of reads.

Showing ¹²/₁₂ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
ZEKI0001	0.07%	61.07%	38.93%	0.20	remove polyAT
ZEKI0002	0.07%	61.87%	38.13%	0.18	remove polyAT
ZEKI0003	0.08%	62.69%	37.31%	0.21	remove polyAT
ZEKI0004	0.07%	61.48%	38.52%	0.20	remove polyAT
ZEKI0005	0.08%	62.26%	37.74%	0.21	remove polyAT
ZEKI0006	0.07%	58.35%	41.65%	0.19	remove polyAT
ZEKI0007	0.07%	60.10%	39.90%	0.18	remove polyAT
ZEKI0008	0.07%	60.14%	39.86%	0.19	remove polyAT
ZEKI0009	0.07%	63.47%	36.53%	0.19	remove polyAT
ZEKI0010	0.06%	56.82%	43.18%	0.17	remove polyAT
ZEKI0011	0.07%	60.66%	39.34%	0.20	remove polyAT
ZEKI0012	0.07%	58.63%	41.37%	0.19	remove polyAT

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Pt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Pt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Pt_%_R2_BP_Lost1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Pt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Pt_Notes1`	None

hts_NTrimmer

Trims reads to the longest subsequence that contains no N's.

Showing ¹²/₁₂ rows and ⁵/₅ columns.

Sample Name	Total Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	% Discarded	Notes
ZEKI0001	382222	87.77%	12.23%	0.00%	remove any remaining N bases
ZEKI0002	274804	87.82%	12.18%	0.00%	remove any remaining N bases
ZEKI0003	401067	87.61%	12.39%	0.00%	remove any remaining N bases
ZEKI0004	381633	87.71%	12.29%	0.00%	remove any remaining N bases
ZEKI0005	447675	87.04%	12.96%	0.00%	remove any remaining N bases
ZEKI0006	383837	87.83%	12.17%	0.00%	remove any remaining N bases
ZEKI0007	400141	87.74%	12.26%	0.00%	remove any remaining N bases
ZEKI0008	400764	88.04%	11.96%	0.00%	remove any remaining N bases
ZEKI0009	298800	89.42%	10.58%	0.00%	remove any remaining N bases
ZEKI0010	473563	88.03%	11.97%	0.00%	remove any remaining N bases
ZEKI0011	340289	87.57%	12.43%	0.00%	remove any remaining N bases
ZEKI0012	310238	86.97%	13.03%	0.00%	remove any remaining N bases

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Sort	Group	Column	Description	ID	Scale
\|\|	Total Bp Lost	Total Bp Lost	Total input bps (SE and PE) trimmed.	`Nt_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R2_BP_Lost1`	None
\|\|	% Discarded	% Discarded	Percentage of Reads (SE and PE) Discarded	`Nt_%_Discarded1`	None
\|\|	Notes	Notes	Notes	`Nt_Notes1`	None

NTrimmer: Trimmed Basepairs Composition

Plots the number of N bases trimmed from ends of paired end and single end reads.

hts_LengthFilter

Discards reads below a minimum length threshold.

Showing ¹²/₁₂ rows and ²/₂ columns.

Sample Name	% PE Lost	Notes
ZEKI0001	0.28%	remove reads < 50 bp
ZEKI0002	0.44%	remove reads < 50 bp
ZEKI0003	0.52%	remove reads < 50 bp
ZEKI0004	0.52%	remove reads < 50 bp
ZEKI0005	0.67%	remove reads < 50 bp
ZEKI0006	0.74%	remove reads < 50 bp
ZEKI0007	0.54%	remove reads < 50 bp
ZEKI0008	0.52%	remove reads < 50 bp
ZEKI0009	0.62%	remove reads < 50 bp
ZEKI0010	0.27%	remove reads < 50 bp
ZEKI0011	0.48%	remove reads < 50 bp
ZEKI0012	0.63%	remove reads < 50 bp

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		% PE Lost	% PE Lost	Percentage of Paired End Reads Lost	`Lf_PE_loss1`	None
\|\|		Notes	Notes	Notes	`Lf_Notes1`	None

hts_Stats 2

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ¹²/₁₂ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
ZEKI0001	100.00%	97.35%	97.18%	44.22%	0.0000%	final stats
ZEKI0002	100.00%	97.55%	97.42%	44.99%	0.0000%	final stats
ZEKI0003	100.00%	97.36%	97.12%	44.35%	0.0000%	final stats
ZEKI0004	100.00%	97.53%	97.12%	44.60%	0.0000%	final stats
ZEKI0005	100.00%	97.49%	96.99%	44.59%	0.0000%	final stats
ZEKI0006	100.00%	97.63%	97.27%	44.73%	0.0000%	final stats
ZEKI0007	100.00%	97.56%	97.07%	44.98%	0.0000%	final stats
ZEKI0008	100.00%	97.58%	97.09%	44.87%	0.0000%	final stats
ZEKI0009	100.00%	97.59%	96.99%	45.20%	0.0000%	final stats
ZEKI0010	100.00%	97.81%	97.43%	44.59%	0.0000%	final stats
ZEKI0011	100.00%	97.41%	96.95%	44.82%	0.0000%	final stats
ZEKI0012	100.00%	97.30%	96.63%	45.07%	0.0000%	final stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction2`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q302`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q302`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content2`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content2`	None
\|\|	Notes	Notes	Notes	`St_Notes2`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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chmiel_human_rnaseq

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chmiel_human_rnaseq

General Statistics

General Statistics: Columns

STAR

Alignment Scores

Gene Counts

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

Basepair Reduction

hts_Stats

Table Nmsf: Columns

Read Lengths: Paired End

Table Tnrj: Columns

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener

hts_SeqScreener 2

Table Odej: Columns

hts_SuperDeduper

Table Ftqg: Columns

SuperDeduper: Duplicate Saturation

hts_AdapterTrimmer

Table Yrwl: Columns

AdapterTrimmer: Trimmed Basepairs Composition

hts_QWindowTrim

Table Nqcz: Columns

QWindowTrim: Trimmed Basepairs Composition

hts_PolyATTrim

Table Dbsk: Columns

hts_NTrimmer

Table Lrpw: Columns

NTrimmer: Trimmed Basepairs Composition

hts_LengthFilter

Table Imwv: Columns

hts_Stats 2

Table Hnuy: Columns

Read Lengths: Paired End

Base by Cycle: Paired End

Quality by Cycle: Paired End

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